De novo network analysis reveals autism causal genes and developmental links to co-occurring traits

In this study, we provide a biological argument for looking at an autistic individual’s phenotype as being related to their combined genetic risk for different clusters of traits.

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Thank you for this interesting contribution to Life Science Alliance. We are looking forward to receiving your revised manuscript. --An editable version of the final text (.DOC or .DOCX) is needed for copyediting (no PDFs).
--High-resolution figure, supplementary figure and video files uploaded as individual files: See our detailed guidelines for preparing your production-ready images, https://www.life-science-alliance.org/authors --Summary blurb (enter in submission system): A short text summarizing in a single sentence the study (max. 200 characters including spaces). This text is used in conjunction with the titles of papers, hence should be informative and complementary to the title and running title. It should describe the context and significance of the findings for a general readership; it should be written in the present tense and refer to the work in the third person. Author names should not be mentioned.
--By submitting a revision, you attest that you are aware of our payment policies found here: https://www.life-sciencealliance.org/copyright-license-fee Full guidelines are available on our Instructions for Authors page, https://www.life-science-alliance.org/authors We encourage our authors to provide original source data, particularly uncropped/-processed electrophoretic blots and spreadsheets for the main figures of the manuscript. If you would like to add source data, we would welcome one PDF/Excel-file per figure for this information. These files will be linked online as supplementary "Source Data" files. ***IMPORTANT: It is Life Science Alliance policy that if requested, original data images must be made available. Failure to provide original images upon request will result in unavoidable delays in publication. Please ensure that you have access to all original microscopy and blot data images before submitting your revision.*** Reviewer #1 (Comments to the Authors (Required)): Thank you for this opportunity to review this manuscript. I consider the work presented here to be excellent. From my perspective the appropriate tools have been used to examine an important question. But more than that, the approach modeled here is crucially important to understanding the basis of complex diseases and is an important step away from a single-gene causative interpretation. I have only minor issues to raise: 1. I am slightly uncomfortable with the term 'causative' as cause has not been proven in this work. 2. the introduction is quite dense, does not emphasize that this work is using human data sets 3. ADHD needs to be defined 4. MAPT encodes tau Reviewer #2 (Comments to the Authors (Required)): Autism is a complex neurodevelopmental condition that manifests in various ways. Autism is often accompanied by other neurological disorders，the role of specific genes in autism, their relationship with co-occurring traits is not fully understood，the author of this paper conducted a two-sample Mendelian Randomisation analysis and identified four genes located at the 17q21.31 locus that are causally linked to autism in fetal cortical tissue (i.e. LINC02210, LRRC37A4P, RP11-259G18.1, RP11-798G7.6). LINC02210 was also identified as being causally related to autism in adult cortical tissue, their results support that an individual's autism phenotype is partially determined by their genetic risk for co-occurring conditions, which could be used to develop predictive models for more accurate diagnosis and better clinical management. However, there are some concerns are not well addressed, therefore, I would strongly suggest the author provide a major revision before acceptance, the comments are as follows: Major concern: 1. Although the author provided four genes located at the 17q21.31 locus that are causally linked to autism in fetal cortical tissue (i.e. LINC02210, LRRC37A4P, RP11-259G18.1, RP11-798G7.6), however, the author failed to verify their function, at least expression measurement. 2. Based on data of this paper, we do not know whether these identified genes are neuronal or nonneuronal expression, inhibitory or excitatory neurons expression. 3. How many samples were used to generate these many data, although we can see that these data were extracted from somewhere, but I think you should provide more detail regarding these samples being used. 4. Are there any differences of these identified genes expression in different gender or sex. 5. Did you check these identified gene expression level in PD, AD and autism, since the author found that LINC02210 and RP11-259G18.1 were associated with PD, AD and autism. 6. Did you evaluate the prevalence of schizophrenia in autistic other populations?
Minor concern: 1. Please provide full name of abbreviated words, such as ADHD, GTEx et. We would like to thank you and the reviewers for the opportunity to modify our manuscript following the constructive criticisms that were raised by the referees. Both referees were positive about our work and their comments have helped us make changes that have improved the quality of the manuscript. We have provided a point-by-point response to the referees below.
We look forward to hearing from you.  1b)."

Sincerely
2. The introduction is quite dense, does not emphasize that this work is using human data sets -We have shortened the introduction and updated the text to emphasise the use of human datasets: "To investigate the interconnectivity of complex polygenic traits, network-based analyses using human derived datasets s have been previously used by our group (Golovina et al. 2023). In this study, we identified causative and pleiotropic genes that are affected by SNPs associated with both autism and other traits within human cortical gene regulatory networks (GRNs) at two different developmental stages." 3. ADHD needs to be defined -We have defined ADHD at first mention: "Common co-occurring conditions reported with autism include attentiondeficit/hyperactivity disorder (ADHD), anxiety, depressive disorders and schizophrenia." 4. MAPT encodes tau 2 -The text has been corrected to state that MAPT encodes tau: "For example, MAPT encodes tau, potentially resulting in the development of tauopathy in the brain (Grigg et al. 2020)." Reviewer 2: 1. Although the author provided four genes located at the 17q21.31 locus that are causally linked to autism in fetal cortical tissue (i.e. LINC02210, LRRC37A4P, RP11-259G18.1, RP11-798G7.6), however, the author failed to verify their function, at least expression measurement.
-The referee is correct, we were unable to verify the function of the four genes located in 17q21.31. Firstly, these genes are non-coding/pseudogenes and we have been unable to extrapolate on their function. We were unable to make direct measures of the expression of these genes in Autistic tissues. However, we modified the manuscript to clarify that these ncRNAs/pseudogenes are expressed in the fetal and adult cortical tissues: 2. Based on data of this paper, we do not know whether these identified genes are neuronal or nonneuronal expression, inhibitory or excitatory neurons expression.
-We regret we have been unable to clarify this. See reply to Reviewer 2 point 1. 3. How many samples were used to generate these many data, although we can see that these data were extracted from somewhere, but I think you should provide more detail regarding these samples being used.
-The data used in this study were obtained from multiple sources (see supplementary table 9 for data accession codes). Information on Hi-C and GTEx sample numbers is best obtained from the relevant references which are provided in the text (GTEx Consortium, 2020;Schmitt et al., 2016;Walker et al., 2019;Won et al., 2016). We have modified supplementary figure 1a to provide the sample details for the GWAS study used for 2SMR.
4. Are there any differences of these identified genes expression in different gender or sex.
-We thank the reviewer for their suggestion. This is something we often discuss, however, we have not yet investigated it largely due to limitations with our current datasets. We hope to be able to address this with appropriate datasets in a future study. 5. Did you check these identified gene expression level in PD, AD and autism, since the author found that LINC02210 and RP11-259G18.1 were associated with PD, AD and autism.
-We have information in independent studies that indicate there is some convergence on causal genes in the 17q21.31 locus in PD. This is currently in preparation. We regret that we have not yet analyzed AD. 6. Did you evaluate the prevalence of schizophrenia in autistic other populations?
-We have not investigated the prevalence of schizophrenia in autistic other populations. This was outside the scope of this study. 7. Please provide full name of abbreviated words, such as ADHD, GTEx et. Thank you for submitting your revised manuscript entitled "De novo network analysis reveals autism causal genes and developmental links to co-occurring traits.". We would be happy to publish your paper in Life Science Alliance pending final revisions necessary to meet our formatting guidelines.
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Thank you for this interesting contribution, we look forward to publishing your paper in Life Science Alliance.